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OMERO.importer Formats

This page lists all the formats currently supported by OMERO.importer

Currently Supported Importer Formats

The OMERO.importer uses the LOCI bio-formats library to support a number of formats. Please note however that we try to extensively test each file format before we add it to the importer, so our success depends on how much test data we have.

As always, contributions of sample data will help to ensure that the OMERO.importer accurately supports a wide range of formats, and any contributions you may wish to make are always welcome by contacting us on our forums here, or our user mailing list here.


NOTE:

As of version 4.1 the OMERO.importer supports the entire range of bio-formats file types. To review what formats are currently supported by bio-formats, see the bio-formats supported lile list.


Format Extensions Added in Version Comments
AVI (Audio Video Interleave) .avi 4.1  
GIF (Graphics Interchange Format) .gif 2.2  
JPEG .jpg 2.2 Older versions of the importer required a third party library do decompress lossless JPEG. See http://trac.openmicroscopy.org.uk/omero/wiki/LosslessJPEG for more information on this issue.
PNG (Portable Network Graphics) .png 2.1  
QuickTime Movie .mov 4.1  
TIFF (Tagged Image File Format) .tif 2.0 This is a very open standard, so expect some variants to be unsupported.
Bio-Rad PIC .pic, .raw, .xml 2.1 Older versions of the the importer could not stitch multiple .pic files into one "combined" image.
EPS (Encapsulated PostScript) .eps, .epsi, .ps 4.1  
ICS (Image Cytometry Standard) .ics, .ids 2.3.1  
Leica LCS LEI .lei, .tif 2.1  
MetaMorph Stack (STK) .stk, .nd 2.1  
Nikon NIS-Elements ND2 .nd2 2.3 ND2 images based on the Lossless JPEG standard require a linked static library in older version of the importer. See http://trac.openmicroscopy.org.uk/omero/wiki/LosslessJPEG for more information on this issue.
3i SlideBook .sld 3.1  
PICT (Macintosh Picture) .pict 2.3  
Zeiss LSM (Laser Scanning Microscope) 510 .lsm, .mdb 4.1  
Adobe Photoshop PSD .psd 4.1  
Analyze 7.5 .img, .hdr 4.1  
Animated PNG .png 4.1  
Aperio SVS TIFF .svs 4.1  
DeltaVision .dv, .r3d 2.1  
DICOM .dcm, .dicom 2.2 Compressed dicoms did may import correctly in older versions of the importer.
FITS (Flexible Image Transport System) .fits 4.1  
Improvision Openlab LIFF .liff 2.2  
JPEG 2000 .jp2 4.1  
Leica LAS AF LIF (Leica Image File Format) .lif 2.1  
Li-Cor L2D .l2d, .tif, .scn 4.2  
MINC MRI .mnc 4.1  
MRC (Medical Research Council) .mrc 4.1  
NIfTI .img, .hdr 4.1  
Olympus FluoView FV1000 .oib, .oif 2.3.1  
Olympus FluoView TIFF .tif 4.1  
PGM (Portable Gray Map) .pgm 2.2  
Zeiss AxioVision ZVI (Zeiss Vision Image) .zvi 2.3.1  
Targa .tga 4.1  
Photoshop TIFF .tif, .tiff 4.1  
Amersham Biosciences Gel .gel 3.0  
Andor Bio-Imaging Division (ABD) TIFF .tif 4.1  
Bitplane Imaris .ims 2.2  
FEI .img 4.1  
Gatan Digital Micrograph .dm3 4.1  
Hamamatsu Aquacosmos NAF .naf 4.1  
ImagePro Sequence .seq 4.1  
Openlab TIFF .tif 2.2  
InCell 1000 .xdce, .tif 4.1  
IPLab .ipl 4.1  
MetaMorph 7.5 TIFF .tiff    
╬╝Manager .tif, .txt 3.1  
Minolta MRW .mrw 4.1  
MNG (Multiple-image Network Graphics) .mng 4.1  
NRRD (Nearly Raw Raster Data) .nrrd, .nhdr, .raw, .txt 2.2  
OME-TIFF .ome.tiff 3.0  
OME-XML .ome 3.0  
PerkinElmer UltraView .tif, .2, .3, .4, ... 2.3.1  
Prairie Technologies TIFF .tif, .xml, .cfg 2.3  
Amira Mesh .am, .amiramesh, .grey, .hx, .labels 4.1  
Improvision TIFF .tif 4.1  
Lambert Instruments FLIM .fli 4.1  
Hamamatsu HIS .his 4.1  
Quesant .afm 4.1  
Molecular Imaging .stp 4.1  
Topometrix .tfr, .ffr, .zfr, .zfp, .2fl 4.1  
JEOL .dat, .img, .par 4.1  
Seiko .xqd, .xqf 4.1  
Oxford Instruments .top 4.1  
LEO .sxm 4.1  
Burleigh .img 4.1  
Unisoku .dat, .hdr 4.1  
BD Pathway .exp, .tif 4.1  
RHK .sm2, .sm3 4.1  
SM Camera   4.1  
SBIG 4.1  
JPK .jpk 4.1  
Gatan Digital Micrograph 2 .dm2 4.1  
WA-TOP .wat 4.1  
Axon Raw Format .arf 4.1  
Alicona 3D .al3d 4.1  
Becker & Hickl SPCImage .sdt 4.1  
Cellomics .c01 4.1  
Evotec/PerkinElmer Opera Flex .flex 4.1  
ImagePro Workspace .ipw 4.1  
Improvision Openlab Raw .raw 4.1  
IPLab-Mac .ipm 4.1  
Khoros VIFF (Visualization Image File Format) Bitmap .xv 4.1  
LIM (Laboratory Imaging/Nikon) .lim 4.1  
NEF (Nikon Electronic Format) .nef, .tif 4.1  
Olympus CellR/APL .apl, .mtb, .tnb, .tif, .obsep 4.1  
PCX (PC Paintbrush) .pcx 4.1  
SimplePCI .cxd 4.1  
TillPhotonics TillVision .vws 4.1  
VisiTech XYS .xys, .html 2.0 Older importers may not fully support all Visitech metadata included in the accompanying html file.
MIAS (Maia Scientific) .tif 4.1  
Nikon EZ-C1 TIFF .tiff 4.1  
Olympus ScanR .xml, .dat, .tif 4.1  
Bio-Rad Gel .1sc 4.1  
Imacon .fff 4.1  
UMB .pr3 4.1  
VG SAM .dti 4.1  
Text .txt 4.1  
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